Actually you can add only one additional folder to check, from Options of Manage Apps tool. We are working to improve it and support automatically MyApps subfolders. If you use the last Suite release, with the automatic manager update enabled, the new Suite Manager version will be automatically installed when available.

Not yet.. actually I'm a little busy, but I have opened the manager source code to allow other users to improve it and propose their improvements. Sources are available at the end of the Suite page.Anyway this feature is in my ToDo list and I'll try to implement it in future.